[pkg-bioc] BioConductor

[Andreas Tille]

Hi,

I would like to have some clarification, what exactly is packaged in the
pkg-bioc group.  At LinuxTage Chemnitz I've got some interesting hint to
BioConductor and I have seen that there is a really interesting collection
of R packages at

     http://www.bioconductor.org/packages/release/bioc/

I know that there is an Alioth project concerning packaging of
BioConductor at

     http://alioth.debian.org/projects/pkg-bioc/

but in SVN

     http://svn.debian.org/wsvn/pkg-bioc/trunk/packages/?rev=0&sc=0

I can only see a package of r-cran-qtl - which is actually not at
BioConductor page (or at least I did not found it there).

If I try to follow the advise how to obtain BioConductor packages
given at

     http://wiki.debian.org/AliothPkgBioc

and just try

     sh ./r_pkg_prepare.sh --create-all --eu

I get a file autogenerate-variable.out and when I continue with

$ ./r_pkg_update.pl --doupdate --dobuilderupdate
Can't locate Graph/Directed.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl . /usr/share/R/share/perl ../tools-ng) at debtag.pm line 140.
BEGIN failed--compilation aborted at debtag.pm line 140.
Compilation failed in require at ./r_pkg_update.pl line 161.
BEGIN failed--compilation aborted at ./r_pkg_update.pl line 161.

so I guess something is wrong.

My suspicion is that this stuf was not touched for a while because
the scripts contain a version string "2.1" for BioConductor and upstream
mentions 2.3 as stable and 2.4 as devel.

So could you please give a short summary about the current status of
this BioConductor stuff here on the list to perhaps coordinate things
to some extend?

Thank you very much for your effort so far

        Andreas.

-- 
http://fam-tille.de